Copper sites in biology activate dioxygen for electrophilic aromatic attack and hydrogen atom abstraction, catalyze the 4-electron reduction of dioxygen to water, and activate substrates for the spin-forbidden reaction with O2. These function as monooxygenases, dioxygenases and oxidases, perform cofactor biogenesis and proton pumping, and generate deleterious reactive oxygen species (ROS). The copper proteins and their study are considered in four classes based on structural type and function: (1) enzymes that have coupled binuclear copper sites; (2) enzymes with multi-metal centers that catalyze the 4-electron reductive cleavage of O-O bonds; (3) enzymes that utilize a single reduced, Cu(I), center to activate O2; and (4) those that require an oxidized Cu(II) center to activate substrates. Intermediates in these systems exhibit unique spectral features that reflect novel geometric and electronic structures that are key to their reactivities. This research program utilizes and develops a wide range of spectroscopic methods and the analyses of unique spectral data to elucidate reaction coordinates that provide fundamental insight into biological function. Our research effort, directed across all four classes of copper proteins, both defines their specific reaction mechanisms and the role of the protein environment in tuning reactivity, and broadly determines why specific active site structures have evolved for their efficient and selective functions in Nature. These studies provide molecular level insight into reactivity, and are of fundamental importance towards understanding pathogenesis and providing structural and mechanistic insight for drug design, medical device development, and the generation of new catalysts.